Restoration of seminatural habitats in the rural agricultural landscape has become an urgent matter in environmental conservation. We propose here a procedure for predicting the trajectory of species recovery and for specifying the priority of habitat types for restoration of a rural agricultural landscape. We then apply it as a case study to the recovery of dragonfly species in the Azame restoration project that began in 2003 in northern Kyushu, Japan. We examined the nestedness of the regional distribution of dragonflies using a national database on wildlife distribution and listed the recorded species in order of their prevalence in the region. We also conducted a census of adult dragonflies currently found at the restoration site to assess species richness. By comparing these data, we identified species potentially capable of inhabiting the restoration site and, based on their habitat requirements, suggest what type of habitat (e.g., bogs and marshes, ponds, and bodies of slow-moving water) should be restored preferentially. We observed significant nestedness in the presence–absence matrix for dragonfly species and thus predict that species recovery at the restoration site will follow the regional order of prevalence of the species. The required habitat types did not differ significantly between the currently observed species and the potential species, which indicates that all these habitat types should be restored in the project.